In 1999 the AFL announced the creation of a new developmental league, af2. Later that year Jacksonville was awarded one of the fifteen charter franchises in the new league.[2] The team was eventually named the Jacksonville Tomcats after the F-14 Tomcat fighter jet, in reference to Jacksonville's historical connection with the U.S. Navy.[3] Ownership was awarded to a group that included owners of the Jacksonville Lizard Kings minor league ice hockey team;[2] Wayne Weaver eventually purchased Jacksonville's proprietary arena football rights.[4]

The Tomcats began play in the 2000 af2 season. The Tomcats had to work around the limitations of the Jacksonville Coliseum, as the venue was too small for arena football regulations; the team reduced their end zones from eight to seven yards, and reduced their five-yard markers to only four yards.[5] In their inaugural season they went 9-7 and made the playoffs, but were eliminated in their first post-season game by the Norfolk Nighthawks. The team sold out all of its home games that year, drawing an average of 8,222 spectators.[4] The following year, the Tomcats again went 9-7, but missed the playoffs. Ticket sales declined that year, a trend that continued in 2002, when the Tomcats went 8-8, again falling short of the playoffs.[4]

The team's mediocre performance, problems with the aging Coliseum, and the rapid expansion of af2, which jumped from 15 teams to 36 in three seasons, contributed to the Tomcats experiencing the league's second worst drop in ticket sales.[6] In 2002 the Tomcats attendance was 6,047, over 2,000 lower than in 2000, and according to then owner Steve Umberger, who also owned the Birmingham Steeldogs, the team had lost several thousand dollars that year.[4] However, team ownership and the Arena Football organization anticipated the construction of the new 15,000-capacity Jacksonville Veterans Memorial Arena, which had broken ground in 2001. After the 2002 season owner Umberger submitted a request to the league for the Tomcats to sit out for the 2003 season, so that they could play in the new Arena the following year, but the league rejected the request.[7] Rather than risk losing more money the next season, and unable to find other interested owners, Umberger decided to fold the team.[4]